


Only Molly Knows

by benedictedcumberbatched



Category: Sherlock (TV)
Genre: Alternate Universe, Canon Compliant, Developing Relationship, F/M, Implied Sexual Content, Songfic, Torture
Language: English
Status: Completed
Published: 2014-12-26
Updated: 2014-12-26
Packaged: 2018-03-03 14:13:47
Rating: Mature
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 5,255
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/2853740
Author URL: https://archiveofourown.org/users/benedictedcumberbatched/pseuds/benedictedcumberbatched
Summary: <blockquote class="userstuff">
              <p>She has always been a constant in Sherlock Holmes's life, the keeper of his secrets and solver of his problems. After all, he was not Sherlock Holmes without Molly Hooper.</p>
            </blockquote>





	Only Molly Knows

**Author's Note:**

> Nothing belongs to me as always. I'm just borrowing the characters from Arthur Conan Doyle and the BBC, and borrowing the song from Travis.
> 
>  
> 
> Many thanks to mizjoely for the betaing!

“What do you need?”

“If I wasn’t everything that you think I am – everything that I think I am – would you still want to help me?”

“What do you need?”

“You.”

_When the day is done_  
Oh Molly Molly  
Will I be the one 

They slaved through the night, going over each and every aspect of every plan. It had to be perfect, every last detail carefully crafted to ensure his survival. He couldn’t trust John or Lestrade with such a task, both of whom he was certain were targets. But she, the one who counted, the one he trusted, the one who dealt with all manners of death in a different way, he could rely on her to achieve his goal. 

But as he stood on the edge of the building, the taunting voice of his equal long since extinguished, he had that fleeting doubt. Would he survive? Would their plan hold out? Spreading his arms out to his side, ignoring the yell that came from the street, he leaned forward and slipped over the edge. 

_When the day is through_  
Oh Molly Molly  
Will I be with you 

“Hold still!” she scolded, drawing her hand away from the scrape on his forehead, just at the edge of his hairline. He just bowed his head and held still, flinching every time she pressed too hard with the cloth as she carefully wiped away all the blood. It wasn’t his of course, even if it was his type, but that didn’t mean he didn’t have bruises. Even with their plan having gone perfectly, there was always that small window for error.

His head bowed, his curls pushed back from his forehead as she scrubbed at a particularly caked on spot, he allowed himself the moment to look at her through his eyelashes. Her eyes were screwed up in concentration, the tip of her tongue sticking out of the corner of her mouth. The feel of her fingers pressed against the top of his head as she held him still was almost grounding. He had always taken her for granted, always used her innocent schoolgirl crush on him to wheedle body parts and lab time and coffee, simply because he could and he knew she wouldn’t say no. But that conversation in the lab, her deducing him, he saw her differently, making him realize how much he had underestimated her. 

She lowered her hand, tossing the cloth onto the counter. She looked down at him, taking his chin in her hand as she turned his head from side to side, checking to make sure she got all the blood off. Sighing, she stepped back, her hand falling from his chin, but he reached out, wrapping his hand around her wrist. He could feel the steady thrum of life beneath her skin, the warmth and softness of the inside of her wrist. He swallowed hard, looking up at her as she watched him warily. He tugged on her wrist, pulling her toward him until she stood between his knees. He replaced her hand back against his cheek, sagging as he felt the light pressure of her fingertips grace over his cheekbones, and over the shell of his ear. She whispered his name, a question. 

With a short gasp, he slipped off the toilet and stood up, her hand falling from his face. He walked out of the bathroom and to her couch without a word. Closing his eyes he memorized the feel of her fingers on his skin and stored it in a room that was growing too large and out of his control.

_Tell me what to do_  
Oh Molly Molly  
Let me follow through 

He sat up with a jerk as he looked around, his chest heaving as he struggled to catch his breath. The flat was dark and quiet, with only the muted glow of the lights outside to dimly light the room. He kicked his feet, a blanket falling to the floor. He couldn’t remember seeing it before and smiled softly to himself as he picked it up and set it on the cushion beside him. Rubbing a hand over his face, he picked up his new mobile; left with the clothes he was able to change into after he jumped. A text alert illuminated the screen and with a pressing together of his lips at the message, he tossed the phone onto the blanket before getting to his feet. 

Quietly he crept down the hallway to her bedroom. He had been here a time or two before, hiding out in her guest bedroom when he had first been released from rehab. He didn’t want to spend all his time with his brother, so he snuck out, seeking out the timid specialist registrar he had met the day before he disappeared for three months. She hadn’t shunned him or pitied him. She just carried on as if nothing had happened and so had he. It was best to keep those emotions and memories hidden anyway. But the night brought those images back and with them, the cracks in his walls began to widen. 

He pushed open the door, pleased she didn’t stir as he poked his head inside. He had watched her sleep once before, but only on the couch that he had just vacated. He wet his dry lips, watching the gentle rise and fall of her chest, her hands curled into fists as she lay on her side, facing him. He knew he should move on, prepare for his departure in a few hours, if the text from his brother was anything to go by. Instead, his feet seemed to move him forward, reaching behind him to shut the door quietly. He crept to the side where she wasn’t lying, lifted the covers, and slid under. He watched her sleep, her breath ghosting over his nose and hands as he faced her. There was something about the way people looked when they were sleeping. Their guard was down, everything on display; every flicker of emotion predominately in dreams would emerge in every twitch of the lips and crinkle of the nose. 

He reached forward and brushed a strand of hair that had fallen in front of her face away. She stirred at his touch, a faint mumble of his name groggy with sleep broke the still between them. He whispered an affirmation and slowly her eyes opened, trying to focus in the dim light. 

“Wha’s wrong?” she mumbled, rubbing her eyes with a fist.

“Nothing, I just…” he trailed off, shifting his gaze away from her. It was suddenly stifling, their close proximity making it difficult for him to think. He shifted away, throwing the blanket off him before swinging his legs to hang over the edge of the bed. 

A hand wrapped around his wrist as he made to stand. She was sitting up now, the sheets pooled around her waist as she watched him warily. He looked over his shoulder at her, her face blank as she waited for him to do something first. 

Taking a deep breath, she fixed him with the very stare he saw only twenty-four hours earlier. “What do you need?” she asked him again, her voice hushed.

He closed his eyes; his shoulders sagged as he crawled back into bed, facing her. Hesitating, he raised his hand and brushed his fingertips lightly along her cheek, her jaw line, over her lips. “You…” he whispered, leaning forward slightly to press his lips to hers. 

_'Cos I am lost at sea_  
Oh Molly Molly  
Haven't got a clue 

He was quiet as he carefully peeled the blankets off himself and swung his legs over the edge of the bed. He reached down to the floor, grabbing his pants and pulling them up, standing as he settled them on his waist. He turned and looked back at her as he adjusted the blankets to cover her once more. She was sleeping soundly on her side facing away from him. In the dim light of dawn peeking through the blinds the pale, smooth skin of her back appeared to glow. Her long hair, usually pulled back neatly from her face in a ponytail, was an absolute mess, but she had never appeared more beautiful. 

Shaking his head, he turned his back and finished retrieving his clothing, piece by piece slipping them back on. His mobile was still in the living room and once dressed again, tugging at the bottom of his jacket to straighten it, he carefully opened the door and stepped out of the room. He left it open. Perhaps he was hoping she would wake before he left, but he reasoned it was so he could hear her if she stirred. 

Picking up his phone, he swiped his thumb across the lock screen and sighed as he saw the message waiting for him. 

_6:30_

He glanced at the time at the top of his phone and closed his eyes. 6:15. Fifteen more minutes before he would be gone, as if he really had died yesterday. He dropped his phone into the pocket of his coat and began rummaging around. Acquiring a pen and using the back of an envelope, he began to write. 

At 6:30, his phone vibrated once more. He didn’t even bother to check it; he knew who it was and what it said. Quietly, he crept back to her room. Standing beside her side of the bed, he placed the envelope where his head had rested over the past few hours. He wanted to wake her, to see her warm brown gaze once more, but if he did, he wouldn’t be able to leave. Leaning down, he brushed a piece of hair from her forehead and tucked it behind her ear. He silently pressed his lips to her temple, allowing his eyes to close for a moment as he breathed in the scent of her hair and of what had occurred. 

He turned and left the room, leaving the door open as he grabbed his long coat and scarf, knowing he could dump them on his brother for a bit of dry cleaning, not that he had much use for them wherever he was off to first. As his hand rest on the doorknob, he bowed his head. “Thank you,” he murmured, before opening the door and stepping out into the dawn without looking back.

_All I have to show_  
For all the years below  
Only Molly knows 

The hardest thing about being away was not being able to have any contact. It was surprising really, to think that where he once thought that alone protected him was the one thing he was absolutely despising at that moment. There were times when his leads on a certain branch of Moriarty’s criminal web would run cold and he would be stuck in some run-down hovel. In his boredom, his mind would wander. He would remember the soft glow of her skin in the pre-dawn light; remember the way her lips molded to his. He would remember the smell of her skin and the taste of her in the back of his throat. If he closed his eyes, he would see her wide brown eyes staring up at him, feel her breath on his face as he moved slowly within her. He would hear the sweet mewls and breathless gasps he had pulled from her body. He would remember her gasping cry that he had swallowed when he roughly pressed his lips to hers as she climaxed, he following shortly thereafter with a loud groan and shuddering of his hips. 

It was only then his eyes would open and he would frown down at his waist, refusing to relieve himself of what he had always considered a trivial experience. He didn’t have to close his eyes to remember the soft gaze she had as she stared up at him, her cheeks flushed, her fingertip tracing along his cheek. Frankly he found he missed it, missed her.

Secretly, he cherished those runaway thoughts on those nights of boredom, although he kept them buried deep when he wasn’t in the somewhat private nature of his latest abode. However, he couldn’t help but wonder if she thought of them too.

_When the lights go down_  
Oh Molly Molly  
Will you be around 

He often thought about London. As an Englishman, he should be used to the cold and the damp, but the damp he felt now, that aching that appeared to seep into the bones and settle there, freezing the marrow, was more than he could bear. Teeth chattering, he pulled the ratty blanket tighter around his shoulders as he lay curled on his side. What he wouldn’t give to be in Baker Street, sitting in his chair before the fire with a cup of tea from Mrs. Hudson. Even in his most intense moments of his work, Baker Street was a place he could escape to. He had John there after all, his moral compass. But Baker Street and its occupants weren’t the only things good about London; there was his other home. He hoped his microscope hadn’t been packed away. He remembered the lab exactly as it looked when he last saw it. Diagrams and medical records scattered about while they had worked through the night. 

He didn’t like change; it meant rearranging things upstairs and that took more time than he wanted to commit to it. The work was everything and without it, he was nothing. But as he sniffed in the cold of Helsinki, the low glow of embers in the grate, he closed his eyes and began to shift the latest changes around. He paused at the door he had closed after Alexandria a year before. He had once told The Woman that sentiment was a chemical defect found on the losing side. His brother had told him that caring wasn’t an advantage. He could remember clearly that moment of weakness where his fingers numbly, and seemingly of their own accord, pushed the buttons on his phone. He hesitated as he heard the dial tone, before raising the mobile to his ear.

“Hello?”

He clutched the phone tighter; his eyes squeezed shut as he allowed himself to breathe.

He said her name, his lips twitching as he heard her gasp, his name a whisper over the phone.

“What are you doing? What if your brother finds out?” she hissed.

He swallowed hard, his hand squeezing the phone harder, as if it were an artery that needed to be held shut until it could be stitched closed again. “I…” he hesitated, his voice cracking. He cleared his throat before trying again. “I just needed to hear your voice. I know it’s late, or early, I don’t know what it is honestly. But just talk, please,” he said quietly, his hand loosening as he heard her moving around, the scrape of metal legs on a tile floor. She was at work. She must be. 

He listened as she spoke, telling him of the bodies she’s been taking care of over the past…how long had it been? He drew the phone away from his ear and read the date at the top of the screen. It had been six months since he left. He didn’t ask about anyone. His name, coming from the speaker had him pulling the phone back up to his ear. 

“Yeah?”

“Is everything alright? You’re awfully quiet…” she trailed off.

“I’m fine. Just thinking,” he replied. 

He remembered how they fell into silence; he could hear the tapping of her fingers against metal. They hung up shortly after.

He didn’t tell her about the woman he failed to save, his contact that looked like her. 

_When the lights are gone_  
Oh Molly Molly  
Will you leave the town 

He shouldn’t have returned to London. Lightning flashed across the sky as he stood across the street under the awning of a café. The windows of the flat were dark, no movement of shadows behind the closed curtains. How often had he dreamt of returning to this flat, of being in this flat with her staring up at him as he loomed over her? He sighed as he stood watch, disguised as a homeless person, not that it was hard to do with his longer than usual hair, dirty face, and ragged clothes. He had seen her of course, when she had arrived home from work. She looked well, same as always but perhaps with a bit more spring to her step. He tried to deduce her, but couldn’t get too close for fear of recognition. No one could know he was in town. 

But he wanted her to know. He wanted to do nothing more than walk up those steps, press the little button with her name next to it, and say her name, to feel his tongue caress the syllables, those three consonants and two vowels. He wanted to hear her chastise him for being so reckless but still welcome him in anyway asking him if he wanted a cup of tea. He had come close three times since that he found himself on her street. It was when a man had come to the door, and waited to be let in did he find himself watching her windows. He couldn’t explain why it felt like someone had just popped a balloon in his chest when he saw the male shadow in her living room window, when he saw the lights go out in the flat as shadows crossed into her bedroom. 

So instead, he stood outside the flat, keeping watch, feeling relieved that she was safe, but wondering if after a year and a half, she had finally gone against his once relevant advice and moved on. 

As he staggered to his feet and prepared to leave in the pre-dawn hours, he rubbed his knuckles over his sternum, unsure why his chest ached as he turned and walked away. His hand shook and he told himself it was only because he needed a cigarette.

_Tell me what is wrong_  
Oh Molly Molly  
Let me sing a song 

He couldn’t get London out of his head. His brief jaunt back to his home, to get a glimpse of his life before, had left him with a feeling of incompleteness, especially when he returned to his task. Sheltered in a dark ground floor flat in Jozsefvaros in Budapest, he leaned against the wall, a file open on his lap. But his mind wasn’t in it. Instead, his eyes were closed, his fingers moving of their own accord as if over the fingerboard of his violin. He could see the black notes on the backs of his eyelids as he composed, a way to allow himself to focus, to relax, to remember. 

_'Cos I have lost the will_  
Oh Molly Molly  
Cannot carry on 

With every punch and slap he took, instead of stars he saw brown eyes floating before him. The man’s voice, harsh with broken English, continued to grate at his ears. With one good punch to the face, he almost groaned out her name, almost put her at risk. But he wouldn’t do that. Instead, he let her name bounce around his brain, let the warmth of her eyes and the sweetness of her smile warm him from the center of his chest and outward to his finger tips. 

If he was about to die, he wanted to remember her face as his final thought.

_All I have to show_  
For all the years below  
Only Molly knows 

He knew that the key to a good disguise was being able to hide in plain sight. But with her and revealing that he was back, no disguises were needed. He felt a twinge in his lip to remind him of that. John would forgive him, eventually, he knew that much. But the fact remained that despite his best, albeit comical intentions disguises were definitely a no-go.

He crept through the hallways of the lower levels of St. Bart’s, peering around corners before he breeched the next hallway to ensure no one else had seen him. He heard footsteps, footsteps he had heard many times before on those tile floors. The same footsteps that had echoed through the hallways of his mind palace for months. 

As he stepped into the doorway of the locker room, his breath caught. She looked the same albeit tired from a long shift. He just stayed put, looking into the mirror on her locker door. He smiled as she gasped, turning around to face him. A small coy smile spread across her lips. 

With a low voice, he said her name. Her smile widened as she took the few short steps toward him, him meeting her in the middle. She raised her hand and brushed it over his split lip.

“John?” she asked, dropping her hand to rest it at his elbow. 

“Hmm, yes, he wasn’t particularly happy I surprised him,” he replied his nose giving a twinge of remembrance. 

As if at the same time, they wrapped their arms around each other. He buried his face in her hair at the top of her head, his hands tightening at the fabric of her lab coat as her clenched at his suit jacket. He could feel rather than hear her muffled voice.

“Welcome home,” she said into his chest before pulling back and looking up at him. His eyes flickered between hers and her lips.

_When the day is done_  
Oh Molly Molly  
Will I be the one 

Her voice floated down the staircase. He still couldn’t believe she was right there, within reach, after months and months of only the wisps of memories stored away in her room of his mind palace.

“What was today about?”

“Saying thank you.”

“For what?”

“Everything you did for me.”

“It’s okay. It was my pleasure.”

“No. I mean it.”

“I don’t mean ‘pleasure’. I mean, I didn’t mind. I wanted to.”

She didn’t get it. She had to know. He had to tell her somehow. “Moriarty slipped up. He made a mistake. Because the one person he thought didn’t matter at all to me was the one person who mattered the most. You made it all possible. But you can’t do this again can you?” 

“I had a lovely day. I’d love to – I just…um…” 

He watched as her gaze dropped to her hands. He looked down, a tightness twisting his insides as he took in the silver band adorned with diamonds in the band with the larger solitaire diamond in the center. It was too big for her, and didn’t suit her, but he bit his tongue on that little bit of information. 

Instead, he said what he figured was expected of him. “Oh, congratulations, by the way.”

He didn’t miss her tense smile before she replied. “He’s not from work.”

He smiled sadly, glad she was too preoccupied with working the ring around her finger to not notice his smile. 

“We met through friends, the old-fashioned way. He’s nice. We…he’s got a dog…we-we go to the pubs on weekends and he…I’ve met his mum and dad and his friends and all his family. I’ve no idea why I’m telling you this.”

“I hope you’ll be very happy. You deserve it. After all, not all the men you fall for can turn out to be sociopaths.”

“No?”

“No.”

He had no idea why he decided to move forward, his gaze fixed on hers as he did so. The emptiness in his chest ached as he gave her a sad smile, genuine and real for him. He leaned forward and kissed her cheek, right near the corner of her lips. He could feel her eyelashes on his cheek as her eyes closed. As he pulled back, he turned away and began to walk from the hallway, not looking back. He went through the doors and sniffed in the cold, winter air, drawing his coat tighter around him against the snow. He could sense her behind him but continued walking, his head down.

Oh how he wished he had heard running footsteps behind him, instead, listening as her soft footfalls faded in the opposite direction.

_When the day is through_  
Oh Molly Molly  
Will I be with you 

He felt his mouth go dry as he saw her in that bright yellow dress with that gaudy yellow bow in her hair. In the past, he would have deduced the outfit and how much it did nothing for her and how she was over compensating for vying for a man’s attention. But there was no need for attention when she was already engaged. He glanced over her way as he entered the reception hall, quickly turning away as the camera focused on her and the fiancée when they decided to be all-romantic.

As he stood before the guests later after the dinner, his nerves getting the better of him, he couldn’t help but glance at her frequently, seeing the look of concern in her eyes all the while offering him a small smile to encourage him onward. He had to admit though; he hadn’t missed her stabbing her fiancée with a fork and couldn’t help the smug satisfaction at the motion. 

But as he swung his coat around his shoulders upon leaving once the music began and everyone had someone to dance with, he popped the collar and pulled his coat close around him. He couldn’t resist thinking of how beautiful she had looked and wondered why she hadn’t come after him when he saw she had noticed him leaving. 

_Tell me what to do_  
Oh Molly Molly  
Let me follow through 

“Clean?”

He internally cringed as he heard her tone. He had known the moment John had mentioned where they were going that he was in for it. She had been there on his last stint. Subconsciously, perhaps it was because of her and what she offered for him that he got clean. 

His eyes snapped open as her hand connected with his cheek causing him to blink a couple times as she swiftly hit him again before rounding it off with a slap to his other cheek. He had clearly underestimated her strength all those times he watched her work. Who knew she had an arm on her? 

“How dare you throw away the beautiful gifts you were born with. And how dare you betray the love of your friends. Say you’re sorry.”

“Sorry your engagement is over. Though I’m fairly grateful for the lack of a ring,” he replied snidely as he rubbed his jaw. He couldn’t stop the smug victorious feeling settling in his stomach, as he was actually grateful for the lack of a ring and not just because she’d slapped him. He wondered when it had actually happened but as there had only been a month between John and Mary’s wedding and this instance, it obviously hadn’t taken long.

“Stop it. Just, stop it.”

Where was the woman who would never have dared to speak up against him? Where was the woman whose voice wavered when she spoke to him? He couldn’t pinpoint when she had changed, but he guessed it was the night he went to her, desperate and scared although he wouldn’t admit it, to keep him alive as he confronted Moriarty. He had always underestimated her usefulness to him, usefulness he used to manipulate her. But he didn’t have to. He kept him focused on the prize, on what his task was, on his survival. She was more than just his pathologist and he couldn’t believe it had taken him so long to realize it. 

Pushing off the table, he whipped his mobile out to take a call, counting his unbelieved in lucky stars that he was saved from confronting those pesky emotions head on. He could have always denied them anyway on account of the drugs in his bloodstream. 

_Where are we to be tomorrow Molly  
Haven't got a clue_

_Murderer…you are a murderer._ He couldn’t get the words out of his head. He couldn’t face her, couldn’t see her before he was ushered into a dark windowed car and driven to the tarmac. He supposed this was the better option of the two he was given; at least he had six months to live compared to mere weeks he would likely have been facing by going to prison and living alongside those he had helped put away. 

But then there was that phone call, the plane turning around and returning to the runway he had just left from four minutes before. “Show me,” he said shortly as he climbed out of the plane and was rushed to the waiting car with the Watsons. Sliding in next to John, he looked at the screen and felt his blood run cold. It was impossible. He simply couldn’t be back. He had watched the man stick a pistol in his mouth and pull the trigger, watched as blood spread across the rooftop. 

But as he stared at the face and listened to the modified voice repeating that same phrase did you miss me…Did you miss me… he slammed the car door shut. “St. Barts, NOW,” he barked, pressing his hands together beneath his chin as he felt that panic beginning to stir in his chest. 

_All I have to show_  
For all the years below  
Only Molly knows 

By the time the car was pulling up near St. Barts, he was already throwing open the door and running up the pavement. Down the hallway, his shoes squeaking as he skidded to a halt before the morgue door. He threw it open, spotting the dropped bowl of tools, blood smeared on the edge of the autopsy table and around the scattered tools on the floor.

He slowly entered the morgue, his shoes crunching broken glass test tubes she must have been carrying to gain samples from a body. The door swung shut behind him as he released it, moving toward her office. He called out her name, his voice cracking. His hand hovered over the door to her office as he made to open it. He released a deep breath, unsure what he would find within. 

But the door to the morgue swung open and he spun around. He whispered her name hoarsely as he began to move toward her. He grabbed her arm and jerked her toward him, crushing her to his chest. 

“What…” she muttered into his chest as she tried to pull back. “What are you doing here? I had to hear from Greg that you had been exiled!” she began to scold, her voice escalating. 

He didn’t even say anything; he just looked at her, his eyes raking over her figure looking for any sign of injury. “What am I doing here? Where were you?” he yelled, his hands finding her face and cradling it.

She frowned at him as she took in the look on his face. “I was in the loo,” she explained carefully.

He sagged with relief before he leaned forward and pressed his lips hard to hers, ignoring the opening of the doors and the audible gasps of his friends and brother. She was safe, whatever was going on elsewhere was nothing compared to her being safe.

After all, he was not Sherlock Holmes without Molly Hooper.


End file.
